CRISPR-HAWK: Haplotype- and Variant-aware guide design toolkit for CRISPR-Cas.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Current CRISPR guide RNA (gRNA) design relies on reference genomes, ignoring genetic variations.
• This oversight limits the efficacy of genome editing therapies in diverse populations.

Purpose of the Study:

• To develop a framework for designing gRNAs that accounts for individual and population genetic variations.
• To ensure the efficacy and equity of genome editing therapeutics.

Main Methods:

• Developed CRISPR-HAWK, a framework integrating variants and haplotypes into gRNA design.
• Analyzed therapeutic targets across 79,648 genomes to assess variant impact on guide performance.

Main Results:

• Genetic variants substantially alter predicted CRISPR guide performance.
• Identified haplotypes that abolish cutting activity for a sickle cell disease therapeutic guide.
• 82.5% of guides across seven therapeutic loci had variants modifying on-target activity.
• Discovered individual-specific guides created by variants, missed by reference-based methods.

Conclusions:

• Variant-aware gRNA selection is critical for effective and equitable genome editing.
• CRISPR-HAWK enables more precise and personalized therapeutic design.
• Incorporating population diversity is essential for advancing genome editing to clinical applications.